Hi everybody,
for variant calling, i am using samtools mpileup.
as far as i know, mpileup is by default ignoring certain reads (duplicate,
failed QC, non-primary, unmapped).
my question, how is its default handling of single-end and paired-end data?
for paired-end data, i have the impression, it only accepts properly paired
reads and ignores for instance singletons.
what about single-end data?
is it:
1. if it's paired-end data, pileup only properly paired + user defined (-q
-Q) + no QC, no duplicates (default)...
2. if it's single-end, pileup only user defined (-q -Q) + no QC, no
duplicates (default) ????
thanks, chris
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